Natural variation of gene models in Drosophila melanogaster Journal Article


Authors: Kurmangaliyev, Y. Z.; Favorov, A. V.; Osman, N. M.; Lehmann, K. V.; Campo, D.; Salomon, M. P.; Tower, J.; Gelfand, M. S.; Nuzhdin, S. V.
Article Title: Natural variation of gene models in Drosophila melanogaster
Abstract: Background: Variation within splicing regulatory sequences often leads to differences in gene models among individuals within a species. Two alleles of the same gene may express transcripts with different exon/intron structures and consequently produce functionally different proteins. Matching genomic and transcriptomic data allows us to identify putative regulatory variants associated with changes in splicing patterns. Results: Here we analyzed natural variation of splicing patterns in the transcriptomes of 81 natural strains of Drosophila melanogaster with known genotypes. We identified dozens of genotype-specific splicing patterns associated with putative cis-splicing quantitative trait loci (sQTL). The majority of changes can be explained by mutations in splice sites. Allelic-imbalance in splicing patterns confirmed that the majority are regulated mainly by cis-genetic effects. Remarkably, allele-specific splicing changes often lead to qualitative changes in gene models, yielding many isoforms not previously annotated. The observed alterations are typically outside protein-coding regions or affect only very short protein segments. Conclusions: Overall, the sets of gene models appear to be flexible within D. melanogaster populations. The observed variation in splicing patterns are predicted to have limited effects on the encoded protein sequences. To our knowledge, this is the first sQTL mapping study in Drosophila. © Kurmangaliyev et al.
Keywords: adult; controlled study; gene mutation; nonhuman; animal cell; heredity; genetic variability; genotype; drosophila; amino acid sequence; drosophila melanogaster; transcriptome; model; quantitative trait locus; quantitative trait loci; rna splicing; splicing; regulatory sequence; quantitative trait locus mapping; allelic imbalance; female; article; genetic strain; natural variation; gene model
Journal Title: BMC Genomics
Volume: 16
ISSN: 1471-2164
Publisher: Biomed Central Ltd  
Date Published: 2015-03-17
Start Page: 198
Language: English
DOI: 10.1186/s12864-015-1415-6
PROVIDER: scopus
PMCID: PMC4373058
PUBMED: 25888292
DOI/URL:
Notes: Export Date: 4 May 2015 -- Source: Scopus
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  1. Kjong Van Stephan Fritz Lehmann
    22 Lehmann